Jit
Enthusiast computational biologist with business dream !!!
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Kanthida Lab !
Research Interest: Bioinformatics High-throughput and high-dimensional data analysis Microbiome data analysis (Main focus) Next-generation and third-generation sequencing data analysis for genomics Gene expression data...RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
By Abhi 3605 days agohttp://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...DIAL
By Abhimanyu Singh 3297 days agowww.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2641 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
By Abhi 665 days agogithub.com - Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main...Bioinformatician in pipeline development
Are you interested in working with pipeline development in bioinformatics, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers...HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
By Jit 3017 days agonservant.github.io - HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not...MCAT: Motif Combining and Association Tool
By Neel 2614 days agogithub.com - This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C][-s S] [-d] [-ff] [-v V]positive_seq negative_seq positional...dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements
By Jit 2403 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2217 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:
